Genetic Characterization of the Norwegian Apple Collection

Commercial fruit production in Norway is located at around latitude 60 degrees north, demanding a careful choice of adapted cultivars. The most comprehensive collection of apple genetic resources in Norway is being kept in the Norwegian Apple Collection (NAC) at the Njos Fruit and Berry Centre (NJOS). The collection contains around 350 accessions and was recently genotyped with a single nucleotide polymorphism (SNP) array. Curated SNP data were used for the assessment of structure and diversity, pedigree confirmation, and core collection development. In the following SNP analysis, we identified several duplicates and parent-child relationships. Across the geographic regions represented, the collection was equally diverse. Different methods for analyzing population structure were applied. K-means clustering and a Bayesian modeling approach with prior assumptions of the data revealed five subpopulations associated with geographic breeding centers. The collection has a distinct genetic structure and low relatedness among the accessions; hence, two core collections with 100 accessions in each were created. These new core collections will allow breeders and researchers to use the NAC efficiently. The results from this study suggest that several of the accessions in the Norwegian Apple Collection could be of high importance for breeding purposes

Patterns and roles of lignan and terpenoid accumulation in the reaction zone compartmentalizing pathogen-infected heartwood of Norway spruce

Tree defense against xylem pathogens involves both constitutive and induced phenylpropanoids and terpenoids. The induced defenses include compartmentalization of compromised wood with a reaction zone (RZ) characterized by polyphenol deposition, whereas the role of terpenoids has remained poorly understood. To further elucidate the tree–pathogen interaction, we profiled spatial patterns in lignan (low-molecular-weight polyphenols) and terpenoid content in Norway spruce (Picea abies) trees showing heartwood colonization by the pathogenic white-rot fungus Heterobasidion parviporum. There was pronounced variation in the amount and composition of lignans between different xylem tissue zones of diseased and healthy trees. Intact RZ at basal stem regions, where colonization is the oldest, showed the highest level and diversity of these compounds. The antioxidant properties of lignans obviously hinder oxidative degradation of wood: RZ with lignans removed by extraction showed significantly higher mass loss than unextracted RZ when subjected to Fenton degradation. The reduced diversity and amount of lignans in pathogen-compromised RZ and decaying heartwood in comparison to intact RZ and healthy heartwood suggest that α-conindendrin isomer is an intermediate metabolite in lignan decomposition by H. parviporum. Diterpenes and diterpene alcohols constituted above 90% of the terpenes detected in sapwood of healthy and diseased trees. A significant finding was that traumatic resin canals, predominated by monoterpenes, were commonly associated with RZ. The findings clarify the roles and fate of lignan during wood decay and raise questions about the potential roles of terpenoids in signal transduction, synthesis, and translocation of defense compounds upon wood compartmentalization against decay fungi.publishedVersio

Accumulation dynamics of transcripts and proteins of cold-responsive genes in fragaria vesca genotypes of differing cold tolerance

Identifying and characterizing cold responsive genes in Fragaria vesca associated with or responsible for low temperature tolerance is a vital part of strawberry cultivar development. In this study we have investigated the transcript levels of eight genes, two dehydrin genes, three putative ABA-regulated genes, two cold–inducible CBF genes and the alcohol dehydrogenase gene, extracted from leaf and crown tissues of three F. vesca genotypes that vary in cold tolerance. Transcript levels of the CBF/DREB1 transcription factor FvCBF1E exhibited stronger cold up-regulation in comparison to FvCBF1B.1 in all genotypes. Transcripts of FvADH were highly up-regulated in both crown and leaf tissues from all three genotypes. In the ‘ALTA’ genotype, FvADH transcripts were significantly higher in leaf than crown tissues and more than 10 to 20-fold greater than in the less cold-tolerant ‘NCGR1363’ and ‘FDP817’ genotypes. FvGEM, containing the conserved ABRE promoter element, transcript was found to be cold-regulated in crowns. Direct comparison of the kinetics of transcript and protein accumulation of dehydrins was scrutinized. In all genotypes and organs, the changes of XERO2 transcript levels generally preceded protein changes, while levels of COR47 protein accumulation preceded the increases in COR47 RNA in ‘ALTA’ crowns.publishedVersio

The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca

<p>Abstract</p> <p>Background</p> <p>The cultivated strawberry <it>Fragaria ×ananassa </it>is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for <it>Fragaria </it>and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for <it>Fragaria </it>is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC) library.</p> <p>Methods</p> <p>A BAC library, consisting of 18,432 clones was constructed from <it>Fragaria vesca </it>f. <it>semperflorens </it>accession 'Ali Baba'. BAC DNA from individual library clones was pooled to create a PCR-based screening assay for the library, whereby individual clones could be identified with just 34 PCR reactions. These pools were used to screen the BAC library and anchor individual clones to the diploid <it>Fragaria </it>reference map (FV×FN).</p> <p>Findings</p> <p>Clones from the BAC library developed contained an average insert size of 85 kb, representing over seven genome equivalents. The pools and superpools developed were used to identify a set of BAC clones containing 70 molecular markers previously mapped to the diploid <it>Fragaria </it>FV×FN reference map. The number of positive colonies identified for each marker suggests the library represents between 4× and 10× coverage of the diploid <it>Fragaria </it>genome, which is in accordance with the estimate of library coverage based on average insert size.</p> <p>Conclusion</p> <p>This BAC library will be used for the construction of a physical map for <it>F. vesca </it>and the superpools will permit physical anchoring of molecular markers using PCR.</p

Integrative “omic” analysis reveals distinctive cold responses in leaves and roots of strawberry, Fragaria × ananassa ‘Korona’

Copyright © 2015 Koehler, Rohloff, Wilson, Kopka, Erban, Winge, Bones, Davik, Alsheikh and Randall. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. *Correspondence: Stephen K. Randall, Department of Biology, Indiana University–Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN 46202-5132, USA, [email protected] assess underlying metabolic processes and regulatory mechanisms during cold exposure of strawberry, integrative “omic” approaches were applied to Fragaria × ananassa Duch. ‘Korona.’ Both root and leaf tissues were examined for responses to the cold acclimation processes. Levels of metabolites, proteins, and transcripts in tissues from plants grown at 18°C were compared to those following 1–10 days of cold (2°C) exposure. When leaves and roots were subjected to GC/TOF-MS-based metabolite profiling, about 160 compounds comprising mostly structurally annotated primary and secondary metabolites, were found. Overall, ‘Korona’ showed a modest increase of protective metabolites such as amino acids (aspartic acid, leucine, isoleucine, and valine), pentoses, phosphorylated and non-phosphorylated hexoses, and distinct compounds of the raffinose pathway (galactinol and raffinose). Distinctive responses were observed in roots and leaves. By 2DE proteomics a total of 845 spots were observed in leaves; 4.6% changed significantly in response to cold. Twenty-one proteins were identified, many of which were associated with general metabolism or photosynthesis. Transcript levels in leaves were determined by microarray, where dozens of cold associated transcripts were quantitatively characterized, and levels of several potential key contributors (e.g., the dehydrin COR47 and GADb) to cold tolerance were confirmed by qRT-PCR. Cold responses are placed within the existing knowledge base of low temperature-induced changes in plants, allowing an evaluation of the uniqueness or generality of Fragaria responses in photosynthetic tissues. Overall, the cold response characteristics of ‘Korona’ are consistent with a moderately cold tolerant plant

A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist")

Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession "Hillquist" (R. argutus). "Hillquist" is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The "Hillquist" assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the "Hillquist" genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.Peer reviewe

Lokal utprøving av jordbærsorter i Nord-Trøndelag

Et prosjekt for utprøving av jordbærsorter ved Bioforsk Midt-Norge i perioden 2006-2008, blir delvis finansiert av Trønderfrukt og FMLA Nord-Trøndelag. I 2006 ble det følgelig plantet et sortsfelt som vil bli høstet i 2007 og 2008. I tillegg ble det i 2006 høstet i avanserte foredlingsfelter og sortsforsøk som var plantet i 2004 og 2005. Resultatene som rapporteres her er fra felter som er plantet i 2004 og 2005. I den perioden var arbeidet delvis finansiert av FMLA Nord-Trøndelag og Graminor AS. Det er vanskelig å se at noe av det nye sortsmaterialet som ble plantet i 2005, kan konkurrere med standardsortene (Korona og Polka). Frida som er svært produktiv og som også smaker godt, blir fort veldig nedsmittet av meldugg på bærene. Muligens yter det dyrkingssystemet vi benytter Frida urettferdighet. Sortene Babette og Hanibal produserer godt, men har ikke den gode smaken som standardsortene har. Seleksjonen PK98.204 (navneforslag: Iris) har også mange svært fine attributter, men når muligens ikke helt opp på grunn av smakskvalitetene. Av nytt sortsmateriale som er utviklet ved Kvithamar på oppdrag fra Graminor, er seleksjonen PK00.335 interessant. Dette er en kryssing mellom Polka og Marmolada og som har vist seg fram med god avling, store bær og fått gode subjektive vurderinger. Den er en sort for hovedsesongen og må derfor konkurrere med Korona og Polka – noe den synes å klare vurdert ut fra tilgjengelig datamateriale. Imidlertid er det nødvendig med flere forsøk før eventuell oppformering starter. Utprøving i mindre skala hos dyrkere burde imidlertid settes i gang.Lokal utprøving av jordbærsorter i Nord-TrøndelagpublishedVersio

Metabolic cold acclimation of 'Polka' and 'Honeoye' strawberries under natural field conditions

The winter hardiness of strawberry varieties used in perennial production systems varies greatly. Still, little information is available on how plant metabolism adapts to cold and freezing temperatures under natural temperature and light conditions. In order to examine the hardening process of overwintering meristematic tissue in Fragaria ananassa, crown samples of field-grown var. ‘Polka’ and ‘Honeoye’ were consecutively collected over a period of 15 weeks, i.e. from the end of the season (week 35/ end August) until midwinter (week 50/ December). Samples were subjected to qGC MS metabolite profiling to assess the reconfiguration of central metabolism, and characterize the regulation of selected compatible solutes. Besides changes in amino acid patterns (glutamic acid, aspartic acid, and asparagine), monosaccharide levels (fructose) increased strongly in ‘Honeoye’ (180 fold compared to start control) towards the end of the acclimation period. In contrast, ‘Polka’ showed a concentration peak (36-fold) in week 47 and a decline towards week 50. Also sucrose levels were steadily increased throughout the cold hardening period with averagely 6-fold higher levels in ‘Honeoye’ compared to ‘Polka’, thus underscoring cultivar-dependent differences. However, both varieties showed a decline in sucrose levels after week 47. Particularly, the raffinose pathway was affected leading to strongly and transiently increased levels of the precursor galactinol (week 42/ mid-October) and the trisaccharide raffinose (weeks 43 to 47/ end October to mid-November). While galactinol biosynthesis was earlier induced in ‘Polka’ (week 38) compared to ‘Honeoye’ (week 39), subsequent raffinose production was delayed in ‘Polka’ (week 47) compared to ‘Honeoye’ (week 45). Major metabolic changes in both varieties coincided with a decrease in day length below 14 h in mid-September, and a consistent drop below 10°C average day temperature by the end of September

Metabolic cold acclimation of 'Polka' and 'Honeoye' strawberries under natural field conditions

The winter hardiness of strawberry varieties used in perennial production systems varies greatly. Still, little information is available on how plant metabolism adapts to cold and freezing temperatures under natural temperature and light conditions. In order to examine the hardening process of overwintering meristematic tissue in Fragaria ananassa, crown samples of field-grown var. ‘Polka’ and ‘Honeoye’ were consecutively collected over a period of 15 weeks, i.e. from the end of the season (week 35/ end August) until midwinter (week 50/ December). Samples were subjected to qGC MS metabolite profiling to assess the reconfiguration of central metabolism, and characterize the regulation of selected compatible solutes. Besides changes in amino acid patterns (glutamic acid, aspartic acid, and asparagine), monosaccharide levels (fructose) increased strongly in ‘Honeoye’ (180 fold compared to start control) towards the end of the acclimation period. In contrast, ‘Polka’ showed a concentration peak (36-fold) in week 47 and a decline towards week 50. Also sucrose levels were steadily increased throughout the cold hardening period with averagely 6-fold higher levels in ‘Honeoye’ compared to ‘Polka’, thus underscoring cultivar-dependent differences. However, both varieties showed a decline in sucrose levels after week 47. Particularly, the raffinose pathway was affected leading to strongly and transiently increased levels of the precursor galactinol (week 42/ mid-October) and the trisaccharide raffinose (weeks 43 to 47/ end October to mid-November). While galactinol biosynthesis was earlier induced in ‘Polka’ (week 38) compared to ‘Honeoye’ (week 39), subsequent raffinose production was delayed in ‘Polka’ (week 47) compared to ‘Honeoye’ (week 45). Major metabolic changes in both varieties coincided with a decrease in day length below 14 h in mid-September, and a consistent drop below 10°C average day temperature by the end of September

Metabolic cold acclimation of 'Polka' and 'Honeoye' strawberries under natural field conditions

The winter hardiness of strawberry varieties used in perennial production systems varies greatly. Still, little information is available on how plant metabolism adapts to cold and freezing temperatures under natural temperature and light conditions. In order to examine the hardening process of overwintering meristematic tissue in Fragaria ananassa, crown samples of field-grown var. ‘Polka’ and ‘Honeoye’ were consecutively collected over a period of 15 weeks, i.e. from the end of the season (week 35/ end August) until midwinter (week 50/ December). Samples were subjected to qGC MS metabolite profiling to assess the reconfiguration of central metabolism, and characterize the regulation of selected compatible solutes. Besides changes in amino acid patterns (glutamic acid, aspartic acid, and asparagine), monosaccharide levels (fructose) increased strongly in ‘Honeoye’ (180 fold compared to start control) towards the end of the acclimation period. In contrast, ‘Polka’ showed a concentration peak (36-fold) in week 47 and a decline towards week 50. Also sucrose levels were steadily increased throughout the cold hardening period with averagely 6-fold higher levels in ‘Honeoye’ compared to ‘Polka’, thus underscoring cultivar-dependent differences. However, both varieties showed a decline in sucrose levels after week 47. Particularly, the raffinose pathway was affected leading to strongly and transiently increased levels of the precursor galactinol (week 42/ mid-October) and the trisaccharide raffinose (weeks 43 to 47/ end October to mid-November). While galactinol biosynthesis was earlier induced in ‘Polka’ (week 38) compared to ‘Honeoye’ (week 39), subsequent raffinose production was delayed in ‘Polka’ (week 47) compared to ‘Honeoye’ (week 45). Major metabolic changes in both varieties coincided with a decrease in day length below 14 h in mid-September, and a consistent drop below 10°C average day temperature by the end of September